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Towards interoperable and reproducible QSAR analyses: Exchange of datasets

QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, bu...

Authors: Ola Spjuth, Egon L Willighagen, Rajarshi Guha, Martin Eklund and Jarl ES Wikberg

Citation: Journal of Cheminformatics 2010 2:5

Content type: Methodology Published on: 30 June 2010
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Erratum to: Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining

Authors: Kristina M Hettne, Antony J Williams, Erik M van Mulligen, Jos Kleinjans, Valery Tkachenko and Jan A Kors

Citation: Journal of Cheminformatics 2010 2:4

Content type: Erratum Published on: 3 June 2010

The original article was published in Journal of Cheminformatics 2010 2:3
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SBE13, a newly identified inhibitor of inactive polo-like kinase 1

Authors: Sarah Keppner, Ewgenij Proschak, Gisbert Schneider and B Spänkuch

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P54

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Rescoring of docking poses using force field-based methods

Authors: Nina M Fischer, WM Schneider and O Kohlbacher

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P52

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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PoseView -- molecular interaction patterns at a glance

Authors: Katrin Stierand and Matthias Rarey

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P50

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Evolutionary design of selective adenosine receptor ligands

Authors: Horst van der Eelke, J Kruisselbrink, A Aleman, MT Emmerich, Andreas Bender and AP IJzerman

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P48

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Fingerprint-based detection of acute aquatic toxicity

Authors: Luca Pireddu, L Michielan, M Floris, P Rodriguez-Tomé and S Moro

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P46

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Semi-empirical derived descriptors for the modelling of properties of N-containing heterocycles

Authors: Alexander Entzian, Horst Bögel, Mirko Buchholz and Ulrich Heiser

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P44

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Automatic pharmacophore model generation using weighted substructure assignments

Authors: Andreas Jahn, H Planatscher, Georg Hinselmann, Nikolas Fechner and A Zell

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P42

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Classification of CYP450 1A2 inhibitors using PubChem data

Authors: Sergii Novotarskyi, Iurii Sushko, R Körner, AK Pandey and Igor Tetko

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P40

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Kernel-based estimation of the applicability domain of QSAR models

Authors: Nikolas Fechner, Georg Hinselmann, A Jahn and A Zell

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P38

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Efficient extraction of canonical spatial relationships using a recursive enumeration of k-subsets

Authors: Georg Hinselmann, Nikolas Fechner, A Jahn and Andreas Zell

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P36

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Progress on an open source computer-assisted structure elucidation suite (SENECA)

Authors: Stefan Kuhn and Christoph Steinbeck

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P34

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Ligand-side tautomer enumeration and scoring for structure-based drug-design

Authors: Thomas Seidel and G Wolber

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P32

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset

Authors: G Marcou, N Lachiche, L Brillet, J-M Paris and A Varnek

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P30

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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OrChem: an open source chemistry search engine for Oracle

Authors: Mark L Rijnbeek and Christoph Steinbeck

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P28

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Picking out polymorphs: H-bond prediction and crystal structure stability

Authors: Peter TA Galek, Frank H Allen and László Fábián

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P26

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Ensemble docking revisited

Authors: Oliver Korb, S Bowden, T Olsson, D Frenkel, J Liebeschuetz and J Cole

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P25

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Fleksy: a flexible approach to induced fit docking

Authors: Markus Wagener, SB Nabuurs and J de Vlieg

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O24

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Virtual screening by high-throughput docking using hydrogen bonding constraints for targeting a protein-protein interface in M. tuberculosis

Authors: Oliver Koch, T Jäger, L Flohé and PM Selzer

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P24

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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High throughput in-silico screening against flexible protein receptors

Authors: Horacio Pérez-Sánchez, Bernhard Fischer, Daria Kokh, Holger Merlitz and Wolfgang Wenzel

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P23

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Approaching the limits: scoring functions for affinity prediction

Authors: Christoph Sotriffer

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O22

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes

Authors: Björn Sommer, T Dingersen, S Schneider, S Rubert and C Gamroth

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O21

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships

Authors: Eugen Lounkine and Jürgen Bajorath

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P21

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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The membrane bound aromatic p-hydroxybenzoic acid oligoprenyltransferase (UbiA) - how iterative improvements lead to a realistic structure that offers new insights into functional aspects of prenyl transferases and terpene synthases

Authors: W Brandt, J Kufka, D Schulze, E Schulze, F Rausch and L Wessjohann

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O20

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Updating existing QSAR models: selection and weighting of new data

Authors: Tomas Öberg and T Liu

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P19

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Personalized information spaces: improved access to chemical digital libraries

Authors: O Koepler, W-T Balke, B Köhncke, I Sens and S Tönnies

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O18

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Integration of chemical information with protein sequences and 3D structures

Authors: Adel Golovin, K Henrick and G Kleywegt

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O17

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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pharmACOphore: multiple flexible ligand alignment based on ant colony optimization

Authors: Gerhard Hessler, Oliver Korb, P Monecke, T Stützle and TE Exner

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P17

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry

Authors: Anthony J Williams, Valery Tkachenko, Sergey Golotvin, Richard Kidd and Graham McCann

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O16

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Mechanistic studies on the ring-opening polymerisation of D,L-lactide with zinc guanidine complexes

Authors: S Herres-Pawlis, J Börner, Vieira I dos Santos and U Flörke

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O15

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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A theoretical investigation of microhydration of amino acids

Authors: Catherine Michaux, J Wouters, D Jacquemin and Eric A Perpète

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P15

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Biomaterialcoatings - a challenging task studied by the molecular fragment dynamics

Authors: Carsten Wittekindt and H Kuhn

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O14

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Making people's lives easier, better and more beautiful - and how computer-aided materials design may help

Authors: Thomas Kostka

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O13

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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CARTESIUS: a group function based toolkit for hybrid molecular modelling

Authors: Mikhail Rudenko and AL Tchougreeff

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P13

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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The protein flexibility in receptor-ligand docking simulations

Authors: Frank Tristram

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O11

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Where are the boundaries? Automated pocket detection for druggability studies

Authors: Andrea Volkamer, T Grombacher and Matthias Rarey

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P11

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Prediction of the partition coefficient between air and body compartments from the chemical structure

Authors: Stefanie Stöckl, R Kühne, R-U Ebert and G Schüürmann

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P9

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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KnowledgeSpace - a publicly available virtual chemistry space

Authors: Carsten Detering, H Claussen, M Gastreich and C Lemmen

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O9

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Comparing manual and automated extraction of chemical entities from documents

Authors: Christian Tyrchan and Sorel Muresan

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P7

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Quantifying model errors using similarity to training data

Authors: Rob D Brown, JD Honeycutt and SL Aaron

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O7

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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A unified approach to the applicability domain problem of QSAR models

Authors: Dragos Horvath, Gilles Marcou and Alexandre Varnek

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O6

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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OCHEM - on-line CHEmical database & modeling environment

Authors: Sergii Novotarskyi, Iurii Sushko, R Körner, Anil Pandey Kumar, Matthias Rupp, VV Prokopenko and Igor Tetko

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P5

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Cross-validation is dead. Long live cross-validation! Model validation based on resampling

Authors: Knut Baumann

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O5

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Representation and searching of biomolecules

Authors: Joeseph L Durant, WL Chen, BD Christie, DL Grier, BA Leland and JG Nourse

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O4

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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jsMolEditor: an open source molecule editor for the next generation web

Authors: L Duan

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P3

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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The role of systems modeling in drug discovery and predictive health

Authors: Eberhard O Voit

Citation: Journal of Cheminformatics 2010 2(Suppl 1):O2

Content type: Oral presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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Dingo: 2D molecule and reaction structural formula rendering library

Authors: Mikhail Kozhevnikov and Boris Karulin

Citation: Journal of Cheminformatics 2010 2(Suppl 1):F2

Content type: Free software session presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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CWM global search - an internet search engine for the chemist

Authors: Alexander Kos and H-J Himmler

Citation: Journal of Cheminformatics 2010 2(Suppl 1):P1

Content type: Poster presentation Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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5th German Conference on Chemoinformatics: 23. CIC-Workshop. November 8-10, 2009, Goslar, Germany

Authors: Frank Oellien, Uli Fechner and Thomas Engel

Citation: Journal of Cheminformatics 2010 2(Suppl 1):A1

Content type: Introduction Published on: 4 May 2010

This article is part of a Supplement: Volume 2 Supplement 1
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